Species identification and delimitation in aquatic plants can be challenging due to their often simple, plastic, and convergent morphology. This has led to varying taxonomic opinions in many genera, including Alisma. One debated case is the narrowly endemic A. wahlenbergii, which occurs submerged in the Baltic Sea region. Depending on the author, it is either accepted at some rank or synonymized with the widespread amphibious A. gramineum. Our study aimed to resolve the status and biogeographic history of this peculiar taxon using herbariomics and environmental niche modelling. Our results indicate that A. wahlenbergii and A. gramineum are best treated as conspecific. Furthermore, the findings suggest that what is considered A. wahlenbergii likely represents two independent colonization events of A. gramineum to the Baltic Sea. Environmental niche models projected onto paleoclimate scenarios suggest that the current main population of A. wahlenbergii in Bothnian Bay was established approximately 8.3–4.2 thousand years ago from the southeast via range expansion through Karelia. The population in the Gulf of Finland is genetically distinct. These results challenge the current view of a single, rare, and endemic taxon of submerged Alisma in the northern Baltic Sea. Instead, it appears that there are two relictual populations of A. gramineum of different origins surviving underwater from a deteriorated climate. Similarly, paleoclimatic projections highlight the significant role of Beringia in explaining the current distribution of A. gramineum in China and western North America. The eastern North American populations seem to have a different and more recent origin.